Biodiversity monitoring is important as it allows to prioritize research into the causes of declines and assessing the efficacy of conservation measures. Regional assessments are valuable, because conservation policies and management are often implemented on national and sub-national level. We analyzed data from the German Common Bird Monitoring for 1990–2018. We derived indices of population size using standard log-linear models, based on point counts and route territory mapping at up to 1200 plots annually. We summarized species trends by ecological trait groups. Among the 93 common breeding birds, farmland birds declined strongly, birds of settlements declined. Forest birds initially declined, but recovered after ca. 2010. Wetland birds increased strongly, albeit the number of species with data was low. Consistent declines were found in ground-nesting birds, granivorous and invertebrate (other than insect)-feeding birds. Trends of insectivorous birds were stable on average, but farmland insectivores declined strongly since the year 2000. Long-distance migrants showed more negative trends compared to short-distance migrants and resident species. Species with narrow habitat niche declined disproportionally. Trends over the entire period were more negative in common species in the dataset (with a German breeding population of > 50 K and < 1 M pairs). On the opposite, short-term trends were more negative in less common species (< 50 K pairs). Cold-adapted species showed largely negative, warm-adapted largely positive trends. Multi-species indicators showed no directional change (i.e., a change from decline to increase or vice versa) conditional on the inclusion or omission of single species, but the magnitude of change was affected in groups with low sample size. This suggests that efforts should be made to develop robust monitoring schemes for rarer species that are not covered by the analyses here. We conclude that conservation policies in Germany should aim at halting the worrying declines in ground-nesting, often insectivorous, farmland birds. The recovery of forest and wetland birds is encouraging, but future trends need to be monitored. Ongoing climate change will affect species directly (via their thermal niche) and indirectly (e.g., through more forest disturbance). Conservation strategies will, therefore, need to consider species adaptation to environmental and climate change, e.g., in better protected area connectivity and management.